TraE - PFAM28P - GREMLIN Contacts

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TraE - TraE protein

PFAM:	PF05309	Sequences: MKLKIFLSKLSNLRAENRLLKLLLLLLLLANLLLALLLYRASKNERVVLVPPTISKEFWVSGNKVSAEYLEQMARYVASLLLNVTPENVDYQFEELLRYVDPEAYGELKAQLAAEAERIKKNNISSVFYPQKIEVDPKTLTVEVTGTLKTYVGDKKVSSERKTYELEFRYRNGRLLLTSFKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	182 (181)
Sequences:	1854 (1502)
Seq/√Len:	111.7
META:	0.798

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
90_D	120_K	4.964	1.00
24_L	27_L	3.132	1.00
16_E	21_K	2.931	1.00
77_V	99_Y	2.903	1.00
52_P	76_Y	2.764	1.00
100_V	108_L	2.674	1.00
128_F	146_G	2.668	1.00
78_A	144_V	2.593	1.00
31_N	34_L	2.592	1.00
20_L	24_L	2.533	1.00
28_L	31_N	2.487	1.00
27_L	31_N	2.452	1.00
89_V	116_A	2.376	1.00
17_N	20_L	2.258	1.00
49_L	58_F	2.205	1.00
141_T	165_E	2.190	1.00
143_E	163_T	2.131	1.00
78_A	166_L	2.023	1.00
54_I	58_F	2.022	1.00
117_E	121_K	2.020	1.00
136_D	139_T	1.987	1.00
59_W	66_S	1.976	1.00
167_E	178_T	1.875	1.00
145_T	163_T	1.825	1.00
141_T	167_E	1.787	1.00
34_L	38_L	1.774	1.00
84_V	119_I	1.746	1.00
151_Y	156_K	1.703	1.00
58_F	72_Q	1.692	1.00
70_L	140_L	1.651	1.00
89_V	93_F	1.642	1.00
149_K	159_S	1.642	1.00
46_R	59_W	1.632	1.00
67_A	137_P	1.630	1.00
97_L	100_V	1.625	1.00
147_T	159_S	1.597	1.00
167_E	179_S	1.592	1.00
67_A	71_E	1.529	1.00
143_E	165_E	1.504	1.00
90_D	116_A	1.503	1.00
79_S	83_N	1.474	1.00
82_L	148_L	1.442	1.00
78_A	82_L	1.424	1.00
74_A	142_V	1.410	1.00
101_D	176_L	1.407	1.00
149_K	156_K	1.399	1.00
145_T	161_R	1.395	1.00
38_L	41_A	1.395	1.00
89_V	119_I	1.384	1.00
77_V	166_L	1.372	1.00
93_F	113_A	1.355	1.00
77_V	177_L	1.347	1.00
156_K	159_S	1.343	1.00
65_V	170_Y	1.322	1.00
82_L	180_F	1.317	1.00
131_Q	161_R	1.315	1.00
101_D	171_R	1.308	0.99
101_D	169_R	1.307	0.99
46_R	61_S	1.306	0.99
126_S	148_L	1.291	0.99
82_L	164_Y	1.288	0.99
129_Y	149_K	1.285	0.99
61_S	64_K	1.284	0.99
80_L	96_L	1.261	0.99
131_Q	147_T	1.219	0.99
17_N	21_K	1.203	0.99
169_R	178_T	1.195	0.99
101_D	178_T	1.192	0.99
97_L	109_K	1.168	0.99
10_L	13_L	1.166	0.99
116_A	120_K	1.166	0.99
69_Y	73_M	1.166	0.99
90_D	94_E	1.157	0.99
25_L	29_L	1.145	0.99
147_T	161_R	1.143	0.99
84_V	89_V	1.141	0.99
119_I	124_I	1.134	0.99
65_V	140_L	1.126	0.98
58_F	66_S	1.118	0.98
84_V	126_S	1.112	0.98
130_P	144_V	1.110	0.98
168_F	175_L	1.094	0.98
5_I	9_K	1.088	0.98
33_L	37_L	1.074	0.98
127_V	151_Y	1.071	0.98
87_E	105_Y	1.063	0.98
118_R	122_N	1.051	0.98
132_K	145_T	1.048	0.98
93_F	112_L	1.038	0.97
86_P	125_S	1.034	0.97
3_L	7_L	1.020	0.97
136_D	141_T	1.019	0.97
110_A	114_A	1.018	0.97
13_L	16_E	0.971	0.96
126_S	150_T	0.965	0.96
74_A	78_A	0.959	0.96
134_E	143_E	0.956	0.96
73_M	175_L	0.955	0.96
30_A	34_L	0.953	0.96
30_A	35_A	0.946	0.95
77_V	168_F	0.941	0.95
90_D	113_A	0.926	0.95
111_Q	115_E	0.925	0.95
74_A	144_V	0.920	0.95
40_R	43_K	0.919	0.95
70_L	73_M	0.915	0.95
7_L	10_L	0.906	0.94
73_M	76_Y	0.904	0.94
166_L	177_L	0.901	0.94
150_T	157_V	0.896	0.94
152_V	157_V	0.890	0.94
4_K	7_L	0.873	0.93
28_L	32_L	0.861	0.93
142_V	168_F	0.854	0.92
148_L	164_Y	0.847	0.92
8_S	11_S	0.842	0.92
44_N	62_G	0.840	0.92
11_S	19_L	0.837	0.92
57_E	66_S	0.835	0.91
20_L	23_L	0.834	0.91
90_D	108_L	0.821	0.91
75_R	133_I	0.820	0.91
2_K	5_I	0.813	0.90
70_L	142_V	0.813	0.90
48_V	59_W	0.812	0.90
83_N	127_V	0.807	0.90
148_L	162_K	0.801	0.90
124_I	157_V	0.793	0.89
5_I	8_S	0.792	0.89
9_K	50_V	0.790	0.89
9_K	12_N	0.789	0.89
14_R	17_N	0.788	0.89
65_V	83_N	0.787	0.89
74_A	168_F	0.786	0.89
75_R	92_Q	0.785	0.89
96_L	100_V	0.784	0.89
73_M	148_L	0.779	0.88
86_P	105_Y	0.770	0.88
49_L	148_L	0.768	0.88
89_V	120_K	0.768	0.88
24_L	28_L	0.767	0.88
24_L	31_N	0.764	0.87
88_N	92_Q	0.764	0.87
73_M	82_L	0.763	0.87
78_A	180_F	0.757	0.87
84_V	93_F	0.755	0.87
7_L	12_N	0.752	0.87
139_T	153_G	0.752	0.87
82_L	100_V	0.751	0.86
60_V	69_Y	0.746	0.86
56_K	72_Q	0.744	0.86
77_V	96_L	0.741	0.86
94_E	98_R	0.728	0.85
23_L	26_L	0.720	0.84
11_S	14_R	0.717	0.84
75_R	175_L	0.712	0.83
75_R	95_E	0.711	0.83
115_E	126_S	0.711	0.83
104_A	107_E	0.708	0.83
52_P	55_S	0.703	0.83
133_I	144_V	0.702	0.83
68_E	71_E	0.699	0.82
120_K	134_E	0.693	0.82
85_T	105_Y	0.688	0.81
71_E	95_E	0.688	0.81
168_F	177_L	0.681	0.81
81_L	111_Q	0.678	0.80
81_L	96_L	0.678	0.80
97_L	105_Y	0.674	0.80
2_K	25_L	0.673	0.80
40_R	44_N	0.670	0.80
49_L	72_Q	0.669	0.79
31_N	37_L	0.669	0.79
33_L	36_L	0.669	0.79
81_L	112_L	0.668	0.79
70_L	135_V	0.667	0.79
22_L	32_L	0.667	0.79
136_D	143_E	0.663	0.79
26_L	32_L	0.662	0.79
60_V	65_V	0.662	0.79
124_I	150_T	0.661	0.79
8_S	29_L	0.659	0.78
114_A	118_R	0.659	0.78
106_G	110_A	0.657	0.78
155_K	164_Y	0.656	0.78
51_P	69_Y	0.651	0.78
21_K	34_L	0.648	0.77
79_S	92_Q	0.648	0.77
4_K	8_S	0.647	0.77
15_A	18_R	0.643	0.77
12_N	15_A	0.642	0.77
45_E	124_I	0.630	0.75
70_L	168_F	0.626	0.75
80_L	92_Q	0.622	0.74
49_L	69_Y	0.621	0.74
18_R	21_K	0.621	0.74
88_N	102_P	0.621	0.74
83_N	129_Y	0.620	0.74
22_L	29_L	0.620	0.74
36_L	42_S	0.619	0.74
144_V	166_L	0.617	0.74
110_A	117_E	0.615	0.73
38_L	66_S	0.613	0.73
49_L	76_Y	0.610	0.73
46_R	62_G	0.608	0.73
107_E	110_A	0.607	0.73
94_E	97_L	0.605	0.72
95_E	98_R	0.602	0.72
81_L	166_L	0.599	0.72
25_L	28_L	0.599	0.72
82_L	146_G	0.598	0.71
50_V	53_T	0.597	0.71
76_Y	95_E	0.595	0.71
72_Q	76_Y	0.591	0.71
115_E	119_I	0.587	0.70
82_L	128_F	0.587	0.70
148_L	180_F	0.586	0.70
107_E	111_Q	0.586	0.70
170_Y	178_T	0.583	0.70
59_W	71_E	0.583	0.70
94_E	138_K	0.581	0.69
84_V	88_N	0.580	0.69
57_E	132_K	0.580	0.69
165_E	179_S	0.576	0.69
50_V	66_S	0.574	0.68
50_V	72_Q	0.574	0.68
84_V	124_I	0.573	0.68
21_K	25_L	0.571	0.68
16_E	19_L	0.571	0.68
35_A	38_L	0.571	0.68
25_L	36_L	0.568	0.68
10_L	14_R	0.567	0.67
33_L	111_Q	0.566	0.67
64_K	94_E	0.564	0.67
45_E	48_V	0.564	0.67
72_Q	82_L	0.561	0.67
111_Q	120_K	0.561	0.67
27_L	30_A	0.559	0.66
84_V	92_Q	0.558	0.66
44_N	47_V	0.556	0.66
29_L	36_L	0.551	0.65
58_F	68_E	0.550	0.65
58_F	76_Y	0.548	0.65
169_R	172_N	0.548	0.65
96_L	116_A	0.546	0.65
87_E	97_L	0.546	0.65
3_L	6_F	0.539	0.64
72_Q	83_N	0.538	0.63
26_L	30_A	0.537	0.63
67_A	135_V	0.537	0.63
79_S	127_V	0.535	0.63
7_L	13_L	0.535	0.63
103_E	171_R	0.534	0.63
170_Y	175_L	0.531	0.62
175_L	178_T	0.525	0.62
55_S	138_K	0.525	0.62
88_N	129_Y	0.525	0.62
23_L	27_L	0.522	0.61
82_L	126_S	0.520	0.61
71_E	133_I	0.520	0.61
34_L	42_S	0.519	0.61
2_K	7_L	0.519	0.61
117_E	120_K	0.516	0.60
52_P	95_E	0.512	0.60
9_K	14_R	0.511	0.59
124_I	156_K	0.508	0.59
166_L	180_F	0.506	0.59
7_L	11_S	0.506	0.59
16_E	22_L	0.505	0.59
54_I	103_E	0.505	0.59
65_V	144_V	0.504	0.58
70_L	175_L	0.500	0.58

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3wz4A	3	0.6593	66.1	0.893	Contact Map
3ub1A	3	0.6099	60.6	0.896	Contact Map
5cnlA	3	0.6538	60.1	0.897	Contact Map
3wz3A	1	0.6374	42.4	0.907	Contact Map
2cc3A	2	0.6429	30.5	0.914	Contact Map
4akzA	1	0.6484	26.8	0.916	Contact Map
4lsoA	1	0.6429	24.4	0.918	Contact Map
4o3vA	2	0.6209	21.2	0.92	Contact Map
2bhmA	2	0.6319	12	0.929	Contact Map
4jf8A	2	0.6593	11.7	0.929	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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